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bad tree structure error when creating a child under a family #2707

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grantfitzsimmons opened this issue Dec 23, 2022 · 3 comments · Fixed by #2753
Closed

bad tree structure error when creating a child under a family #2707

grantfitzsimmons opened this issue Dec 23, 2022 · 3 comments · Fixed by #2753
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@melton-jason
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1 - Bug Incorrect behavior of the product
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7.8.4 (internal b...

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@grantfitzsimmons
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grantfitzsimmons commented Dec 23, 2022 •
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  1. Navigate to this section in the tree:

http://localhost/specify/tree/taxon/?conformation=%7E%7E1%7E204425-%7E181107%7E4690%7E7330-%7E5162-%7E7299%7E194257----%7E2%7E10%7E16%7E617------

Notice that "Chaetodermatidae" is selected.

image

  1. Click "Add Child"
  2. Create a child named "grant-test" and assign it the rank of Genus

image

  1. Click "Save" and you will see this error:
AssertionError at /api/specify/taxon/
bad tree structure

See the expanded error below:
Specify 7 Crash Report - 2022-12-23T21_06_26.336Z.txt

Traceback

/opt/specify7/specifyweb/specify/tree_extras.py in validate_node_numbers
from specifyweb.businessrules.exceptions import BusinessRuleException
from  .auditcodes import TREE_MERGE, TREE_SYNONYMIZE, TREE_DESYNONYMIZE
@contextmanager
def validate_node_numbers(table, revalidate_after=True):
    try:
        validate_tree_numbering(table) …
    except AssertionError:
        renumber_tree(table)
    yield
    if revalidate_after:
        validate_tree_numbering(table)

Seems to be similar to the issue here: #2704

db: UMich_mollusks_2022_12_22
On test panel already
Version v7.7.5

Reported By: Matthew Cruz at UMich
@grantfitzsimmons grantfitzsimmons added 1 - Bug Incorrect behavior of the product pri:unknown labels Dec 23, 2022
@grantfitzsimmons grantfitzsimmons mentioned this issue Dec 23, 2022
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@melton-jason
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melton-jason commented Dec 26, 2022 •
edited by maxpatiiuk
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This issue seems to be of the same vein as #2704 (comment) (Specify found instances where some taxa have children that have the same or higher rank).

I ran the following SQL command and got the following results:

select c.taxonid as childid, p.taxonid as parentid, c.fullname as childName, p.fullname as parentName, c.parentid as childParentID, p.parentid as parentParentID, c.acceptedid as childAcceptedID from taxon c join taxon p on c.parentid=p.taxonid where c.rankid <= p.rankid order by c.fullname;

+---------+----------+--------------------------+-------------------------------------+---------------+----------------+-----------------+
| childid | parentid | childName                | parentName                          | childParentID | parentParentID | childAcceptedID |
+---------+----------+--------------------------+-------------------------------------+---------------+----------------+-----------------+
|      88 |      102 | Acanthochitonida         | Acanthochitonina                    |           102 |             84 |             312 |
|   11687 |    11547 | Aequipecten aequisculata | Chlamys circularis                  |         11547 |           2722 |           20987 |
|   19211 |     4924 | Amphitretus thielei      | Amphitretus pelagicus               |          4924 |           3023 |           20807 |
|   13869 |     8514 | Astarte lens             | Astarte crenata                     |          8514 |           3624 |           20119 |
|    9972 |     8514 | Astarte subequilatera    | Astarte crenata                     |          8514 |           3624 |           20119 |
|    5838 |    19217 | Balcis borealis          | Melanella micrans                   |         19217 |           2761 |           21030 |
|   16606 |    16719 | Bathypolypus proschi     | Bathypolypus arcticus               |         16719 |           3079 |           20559 |
|    8663 |    15962 | Buccinum fucanum         | Buccinum strigillatum               |         15962 |           1444 |           20064 |
|    6993 |    19820 | Bulla occidentalis       | Bulla striata                       |         19820 |           1087 |           20625 |
|   19702 |    19820 | Bulla umbilicata         | Bulla striata                       |         19820 |           1087 |           20625 |
|   12759 |    11711 | Busycon muricatum        | Busycon carica                      |         11711 |           3246 |           20531 |
|   13454 |     5909 | Busycon pyrum            | Busycon spiratum                    |          5909 |           3246 |           20429 |
|    9720 |     4057 | Calliteuthis celetaria   | Histioteuthis celetaria             |          4057 |           1758 |           20879 |
|    7664 |    13555 | Calliteuthis corona      | Histioteuthis corona                |         13555 |           1758 |           20784 |
|   15592 |    13555 | Calliteuthis inermis     | Histioteuthis corona                |         13555 |           1758 |           20267 |
|      14 |       10 | Caudofoveata             | Aplacophora                         |            10 |              2 |              16 |
|   12576 |     4237 | Cerithiopsis taeniolata  | Cerithiopsis metaxae                |          4237 |           2754 |           20719 |
|   19797 |    11713 | Cerithium algicola       | Cerithium eburneum                  |         11713 |           3049 |           20911 |
|   15429 |    10112 | Cerithium biminiense     | Cerithium lutosum                   |         10112 |           3049 |           20758 |
|   19903 |    16089 | Chiroteuthis lacertosa   | Chiroteuthis (Chiroteuthis) veranyi |         16089 |           3797 |           21055 |
|   19534 |     3943 | Chlamys costellatus      | Chlamys islandica                   |          3943 |           2722 |           20190 |
|   12600 |     5413 | Clio caudata             | Clio pyramidata                     |          5413 |           2642 |           20494 |
|   10606 |     5413 | Clio exacuta             | Clio pyramidata                     |          5413 |           2642 |           20494 |
|   12488 |     5413 | Clio lata                | Clio pyramidata                     |          5413 |           2642 |           20494 |
|   19686 |     5413 | Clio lobata              | Clio pyramidata                     |          5413 |           2642 |           20494 |
|   18466 |     5413 | Clio occidentalis        | Clio pyramidata                     |          5413 |           2642 |           20494 |
|   11905 |     6777 | Colus marshalli          | Colus jeffreysianus                 |          6777 |           3161 |           20228 |
|    2496 |     2567 | Compsoteuthis            | Abralia                             |          2567 |            717 |            3766 |
|    5577 |    10528 | Conus fosteri            | Conus villepinii                    |         10528 |           1607 |           20257 |
|   17214 |    18807 | Conus pygmaeus           | Conasprella jaspideus               |         18807 |          40145 |           20452 |
|    9906 |    19066 | Cylichnella eximia       | Acteocina culcitella                |         19066 |           2253 |           20378 |
|   17981 |    15964 | Cymatium pacificum       | Neptunea lyrata                     |         15964 |           1890 |           20598 |
|    9047 |    15511 | Eledonella purpurea      | Bolitaena massyae                   |         15511 |           1069 |           20148 |
|   16082 |    11416 | Elimia laqueata laqueata | Elimia laqueata                     |         11416 |           1219 |           20678 |
|    3096 |     2567 | Enigmoteuthis            | Abralia                             |          2567 |            717 |            3775 |
|   16796 |     5044 | Ervilia rostratula       | Ervilia concentrica                 |          5044 |           3634 |           19975 |
|   13459 |    19191 | Fasciolaria distans      | Fasciolaria lilium                  |         19191 |           3359 |           20304 |
|   17781 |    19191 | Fasciolaria hunteria     | Fasciolaria lilium                  |         19191 |           3359 |           21081 |
|    6273 |    14368 | Goniobasis angulata      | Elimia cahawbensis                  |         14368 |           1219 |           20000 |
|    5120 |    13127 | Goniobasis arachnoidea   | Elimia arachnoidea                  |         13127 |           1219 |           20067 |
|    8078 |    19715 | Goniobasis boykiniana    | Elimia boykiniana                   |         19715 |           1219 |           21083 |
|    9602 |    11416 | Goniobasis castanea      | Elimia laqueata                     |         11416 |           1219 |           20085 |
|   14210 |     4205 | Goniobasis comalensis    | Elimia comalensis                   |          4205 |           1219 |           20511 |
|   17830 |    16136 | Goniobasis crandalli     | Elimia potosiensis                  |         16136 |           1219 |           20984 |
|    5447 |     6299 | Goniobasis ebenum        | Elimia ebenum                       |          6299 |           1219 |           20682 |
|   18740 |     6299 | Goniobasis emeryensis    | Elimia ebenum                       |          6299 |           1219 |           20938 |
|    3984 |    17726 | Goniobasis georgiana     | Elimia lecontiana                   |         17726 |           1219 |           21054 |
|    4214 |     5682 | Goniobasis gracilior     | Elimia livescens                    |          5682 |           1219 |           19921 |
|   16734 |     5682 | Goniobasis haldemani     | Elimia livescens                    |          5682 |           1219 |           20774 |
|   10778 |     5682 | Goniobasis livescens     | Elimia livescens                    |          5682 |           1219 |           21037 |
|    7975 |    19300 | Goniobasis mutabilis     | Elimia mutabilis                    |         19300 |           1219 |           20597 |
|    5168 |    16136 | Goniobasis ozarkensis    | Elimia potosiensis                  |         16136 |           1219 |           19987 |
|    4507 |     6647 | Goniobasis perstriata    | Elimia perstriata                   |          6647 |           1219 |           20995 |
|   10960 |    16136 | Goniobasis plebeius      | Elimia potosiensis                  |         16136 |           1219 |           20433 |
|    8900 |    13127 | Goniobasis spinella      | Elimia arachnoidea                  |         13127 |           1219 |           20885 |
|    8107 |    19715 | Goniobasis viennaensis   | Elimia boykiniana                   |         19715 |           1219 |           20488 |
|    9406 |    17013 | Lacuna glacialis         | Lacuna crassior                     |         17013 |           2344 |           20094 |
|   17371 |    12831 | Lampsilis claibornensis  | Lampsilis straminea                 |         12831 |           1639 |           20585 |
|   10050 |     8708 | Latirus macgintyi        | Latirus carinifer                   |          8708 |           2038 |           20653 |
|   13816 |    16089 | Leptoteuthis diaphana    | Chiroteuthis (Chiroteuthis) veranyi |         16089 |           3797 |           21055 |
|    5913 |    17338 | Littorina arctica        | Littorina obtusata                  |         17338 |           1041 |           20767 |
|    5188 |    19327 | Littorina groenlandica   | Littorina saxatilis                 |         19327 |           1041 |           20814 |
|    9334 |    17338 | Littorina palliata       | Littorina obtusata                  |         17338 |           1041 |           20077 |
|    7568 |    19327 | Littorina rudis          | Littorina saxatilis                 |         19327 |           1041 |           20092 |
|   13254 |    19327 | Littorina tenebrosus     | Littorina saxatilis                 |         19327 |           1041 |           20612 |
|    4625 |    10999 | Loligo reynaudii         | Loligo (Loligo) vulgaris            |         10999 |           3772 |           21064 |
|   15871 |    16089 | Loligopsis veranii       | Chiroteuthis (Chiroteuthis) veranyi |         16089 |           3797 |           20114 |
|    3011 |     2822 | Megastropha              | Helisoma                            |          2822 |            202 |            3791 |
|    3608 |     3601 | Micromenetus             | Menetus                             |          3601 |            202 |            3779 |
|   19866 |    15018 | Neptunea borealis        | Neptunea communis                   |         15018 |           1890 |           20031 |
|   19698 |    15964 | Neptunea obsoleta        | Neptunea lyrata                     |         15964 |           1890 |           20598 |
|    8666 |    15964 | Neptunea pacificum       | Neptunea lyrata                     |         15964 |           1890 |           20598 |
|   16246 |    15964 | Neptunea phoenicia       | Neptunea lyrata                     |         15964 |           1890 |           20598 |
|   15207 |     9239 | Ommatostrephes pacificus | Todarodes pacificus                 |          9239 |           3225 |           20677 |
|   16204 |     9660 | Petaloconchus nigricans  | Petaloconchus varians               |          9660 |           3486 |           19996 |
|    4361 |    10799 | Polypus tenuipulvinus    | Octopus minor                       |         10799 |           2544 |           20062 |
|   13313 |    16140 | Pomacea orinocoensis     | Pomacea glauca                      |         16140 |           1030 |           20601 |
|    4347 |     4126 | Retusa turrita           | Retusa obtusa                       |          4126 |           2346 |           20990 |
|    8574 |    10517 | Simnia vidleri           | Simnia aequalis                     |         10517 |           3348 |           21028 |
|       8 |       10 | Solenogastres            | Aplacophora                         |            10 |              2 |              16 |
|   11353 |     6496 | Spisula alaskana         | Mactromeris polynyma                |          6496 |           2691 |           20765 |
|    7161 |    15932 | Teinostoma invallatum    | Teinostoma supravallatum            |         15932 |           1813 |           19931 |
|    5885 |    16339 | Trophon catalinensis     | Trophon cerrosensis                 |         16339 |           3734 |           20089 |
|   19185 |    10807 | Turbo crenulatus         | Turbo castanea                      |         10807 |           2665 |           20800 |
|    4914 |    15785 | Venus striatula          | Venus gallina                       |         15785 |           2007 |           20952 |
+---------+----------+--------------------------+-------------------------------------+---------------+----------------+-----------------+

@maxpatiiuk
should this Assertion Error be thrown even if the children nodes are synonymized? Was this intended?

The error is thrown here (note this is on the 7.7.5 tag):

specify7/specifyweb/specify/tree_extras.py

Lines 452 to 458 in 6205249

# make sure there are no cycles
cursor.execute((
"select count(*) from {table} t\n"
"join {table} p on t.parentid = p.{table}id\n"
"where t.rankid <= p.rankid\n"
).format(table=table))
assert (0, ) == cursor.fetchone(), "bad tree structure"

@grantfitzsimmons
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grantfitzsimmons commented Dec 27, 2022 •
edited
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Screen.Recording.2022-12-27.at.6.15.52.AM.mov

Still an issue on 7.7.0, 7.7.4, 7.7.5, and 7.8.1.

/opt/specify7/specifyweb/specify/tree_extras.py in validate_node_numbers
from specifyweb.businessrules.exceptions import BusinessRuleException
from  .auditcodes import TREE_MERGE, TREE_SYNONYMIZE, TREE_DESYNONYMIZE
@contextmanager
def validate_node_numbers(table, revalidate_after=True):
    try:
        validate_tree_numbering(table) …
    except AssertionError:
        renumber_tree(table)
    yield
    if revalidate_after:
        validate_tree_numbering(table)

Same major error:

AssertionError at /api/specify/taxon/
bad tree structure

Video is version v7.7.4

melton-jason added a commit that referenced this issue Jan 5, 2023
@melton-jason
Ignore synonymized nodes when checking tree structure
c65dc11 
Fixes #2707
@melton-jason melton-jason mentioned this issue Jan 5, 2023
Merged
melton-jason added a commit that referenced this issue Jan 10, 2023
@melton-jason
Improve the SpecifyExceptionWrapper
48f39f1 
Additionally, provide more data to allow users to diagnose
'bad tree structure' errors so issues like #2704 and #2707
have more context and don't have to run SQL commands to find
the bad nodes.
@melton-jason melton-jason added this to the 7.8.4 (internal bugs) milestone Jan 12, 2023
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This issue has been mentioned on Specify Community Forum. There might be relevant details there:

https://discourse.specifysoftware.org/t/specify-7-8-4-announcement/999/1

@melton-jason melton-jason mentioned this issue Mar 14, 2023
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Ignore synonymized nodes when checking tree structure specify/specify7
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@grantfitzsimmons @melton-jason @specifysoftware